It is necessary to partition eddy covariance measurements of carbon dioxide exchange into its offsetting gross fluxes, canopy photosynthesis, and ecosystem respiration, to understand the biophysical controls on the net fluxes. And independent estimates of canopy photosynthesis (G) and ecosystem respiration (R) are needed to validate and parametrize carbon cycle models that are coupled with climate and ecosystem dynamics models. Yet there is a concern that carbon flux partitioning methods may suffer from spurious correlation because derived values of canopy photosynthesis and ecosystem respiration both contain common information on net carbon fluxes at annual time scales.

We hypothesized that spurious correlation among canopy photosynthesis and ecosystem respiration can be minimized using day–night conditional sampling of CO2 exchange; daytime fluxes are dominated by photosynthesis and nighttime fluxes are dominated by respiration. To test this hypothesis, we derived explicit equations that quantify the degree of spurious correlation between photosynthesis and respiration. Theoretically, day and night samples of net carbon exchange share a different common variable, daytime ecosystem respiration, and the degree of spurious correlation depends upon the variance of this shared variable.

We then applied this theory to ideal measurements of carbon exchange of over a vigorous, irrigated, and frequently harvested alfalfa field in the sunny and windy region of California, the Sacramento-San Joaquin Delta, where soil CO2 efflux is strong. In this case, we found that the correlation coefficient between canopy photosynthesis and ecosystem respiration was −0.79. This relatively high correlation between canopy photosynthesis and respiration was mostly real as the degree of spurious correlation was only −0.32.

We then expanded this analysis to the FLUXNET database that spans a spectrum of climate and plant functional types. We found, on average, that the correlation between gross photosynthesis and ecosystem respiration, using day–night sampling, was close to minus one (−0.828 ± 0.130). For perspective, a large fraction of this correlation was real, as the degree of spurious correlation (Eq. (22)) was −0.526. We conclude that the potential for spurious correlation between canopy photosynthesis and ecosystem respiration across the FLUXNET database was moderate. Looking across the database, we found that the least negative spurious correlations coefficients (>−0.3) were associated with seasonal deciduous forests. The most negative spurious correlations coefficients (<−0.7) were associated with evergreen forests found in boreal climates.